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Establishment and identification of bladder cancer cell sheet 膀胱癌细胞片的建立和鉴定
IF 6 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-09 DOI: 10.1016/j.csbj.2024.07.009
Tuanjie Guo, Zhihao Yuan, Jinyuan Chen, Xiang Wang, Dongliang Zhang
Cell sheet technology (CST) has primarily been applied in tissue engineering for repair purposes. Our preliminary research indicates that an in vivo prostate cancer model established using CST outperforms traditional cell suspension methods. However, the potential for CST to be used with bladder cancer cells has not yet been explored. In this study, we investigated the ability of two bladder cancer cell lines, T24 and 5637, to form cell sheets. We found that T24 cells successfully formed cell sheets. We then performed staining to evaluate the integrity, specific markers, and proliferation characteristics of the T24 cell sheets. Our findings demonstrate that bladder cancer cell sheets can be established, providing a valuable tool for both in vivo and in vitro bladder cancer studies and for personalized drug selection for patients.
细胞片技术(CST)主要应用于组织工程修复。我们的初步研究表明,使用 CST 建立的前列腺癌体内模型优于传统的细胞悬浮方法。然而,CST 用于膀胱癌细胞的潜力尚未得到探索。在本研究中,我们研究了 T24 和 5637 这两种膀胱癌细胞系形成细胞片的能力。我们发现 T24 细胞成功地形成了细胞片。然后,我们对 T24 细胞片的完整性、特异性标记和增殖特征进行了染色评估。我们的研究结果表明,膀胱癌细胞片是可以建立的,这为体内和体外膀胱癌研究以及患者个性化药物选择提供了宝贵的工具。
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引用次数: 0
Direct antiglobulin test type, red blood cell distribution width, and estimated glomerular filtration rate for early prediction of in-hospital mortality of patients with COVID-19 直接抗球蛋白试验类型、红细胞分布宽度和估计肾小球滤过率用于早期预测 COVID-19 患者的院内死亡率
IF 4.4 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-08 DOI: 10.1016/j.csbj.2024.07.002
Fei Chen , Jing Wang , Xinhong Jin , Bin Li , Yili Ying , Yufen Zheng , Guoguang Lu , Jun Li , Bo Shen

Objective

This study aimed to investigate the correlation between COVID-19 and the direct antiglobulin test (DAT) and establish an in-hospital mortality risk predictive model based on the DAT type, which can be used for the early prediction of inpatients with COVID-19.

Methods

In this study, 502 patients admitted to our hospital who underwent DAT testing from January 29 to February 8, 2023, were included (252 DAT-positive and 250 DAT-negative). Among them, 241 cases of COVID-19 were screened(171 DAT-positive and 70 DAT-negative), clinical and laboratory indicators were compared between DAT-positive and DAT-negative groups. Univariate and multivariate logistic regression analysis, the Kaplan-Meier survival curve and receiver operating curves were used to explore the relation between the DAT type and in-hospital mortality of patients with COVID-19.

Results

The proportion of confirmed COVID-19 cases was higher in the DAT-positive group than in the DAT-negative group (67.9 % vs. 28.0 %, P < 0.05). Patients with COVID-19 in the DAT-positive group had higher age-adjusted Charlson comorbidity index scores, red blood cell distribution width (RDW), lactate dehydrogenase, prothrombin time, D-dimer, creatinine, and high-sensitive cardiac troponin T levels than the negative group (P < 0.05), In contrast, hemoglobin and estimated glomerular filtration rate (eGFR) levels were lower in the DAT-positive group. The DAT-positive group also had a higher red blood cell usage volume and in-hospital mortality rate than the DAT-negative group. The mortality rate of patients with COVID-19 with both IgG and C3d positive was higher than that of the other groups. Multivariate logistic regression analysis showed that RDW and eGFR were associated with mortality in patients with COVID-19. The combined predictive model of DAT type, RDW, and eGFR showed an area under the curve of 0.782, sensitivity of 0.769, and specificity of 0.712 in predicting in-hospital mortality risk in patients with COVID-19.

Conclusion

The established predictive model for in-hospital mortality risk of patients with COVID-19 based on DAT type, RDW, and eGFR can provide a basis for timely intervention to reduce the mortality rates of patients with COVID-19. This model is accessible at https://jijijiduola.shinyapps.io/0531// for research purposes.

摘要] 目的 探讨COVID-19与直接抗球蛋白试验(DAT)的相关性,建立基于DAT分型的院内死亡风险预测模型,用于早期预测COVID-19住院患者的死亡。其中,筛查出241例COVID-19(171例DAT阳性,70例DAT阴性),并对DAT阳性组和DAT阴性组的临床和实验室指标进行了比较。采用单变量和多变量逻辑回归分析、Kaplan-Meier生存曲线和接收器操作曲线来探讨DAT类型与COVID-19患者院内死亡率之间的关系。结果DAT阳性组确诊的COVID-19病例比例高于DAT阴性组(67.9%对28.0%,P <0.05)。与阴性组相比,DAT 阳性组的 COVID-19 患者经年龄调整后的夏尔森合并症指数评分、红细胞分布宽度(RDW)、乳酸脱氢酶、凝血酶原时间、D-二聚体、肌酐和高敏心肌肌钙蛋白 T 水平更高(P <0.05),而 DAT 阳性组的血红蛋白和估计肾小球滤过率(eGFR)水平较低。与 DAT 阴性组相比,DAT 阳性组的红细胞使用量和院内死亡率也更高。IgG 和 C3d 均阳性的 COVID-19 患者的死亡率高于其他组别。多变量逻辑回归分析显示,RDW和eGFR与COVID-19患者的死亡率有关。结论基于 DAT 类型、RDW 和 eGFR 的 COVID-19 患者院内死亡风险预测模型的建立可为及时干预提供依据,从而降低 COVID-19 患者的死亡率。该模型可通过 https://jijijiduola.shinyapps.io/0531// 进行研究。
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引用次数: 0
G–PLIP: Knowledge graph neural network for structure-free protein–ligand bioactivity prediction G-PLIP:用于无结构蛋白质配体生物活性预测的知识图谱神经网络
IF 6 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-06 DOI: 10.1016/j.csbj.2024.06.029
Simon J. Crouzet, Anja Maria Lieberherr, Kenneth Atz, Tobias Nilsson, Lisa Sach-Peltason, Alex T. Müller, Matteo Dal Peraro, Jitao David Zhang
Protein–ligand interactions (PLIs) determine the efficacy and safety profiles of small molecule drugs. Existing methods rely on either structural information or resource-intensive computations to predict PLI, casting doubt on whether it is possible to perform structure-free PLI predictions at low computational cost. Here we show that a light-weight graph neural network (GNN), trained with quantitative PLIs of a small number of proteins and ligands, is able to predict the strength of unseen PLIs. The model has no direct access to structural information about the protein–ligand complexes. Instead, the predictive power is provided by encoding the entire chemical and proteomic space in a single heterogeneous graph, encapsulating primary protein sequence, gene expression, the protein–protein interaction network, and structural similarities between ligands. This novel approach performs competitively with, or better than, structure-aware models. Our results suggest that existing PLI prediction methods may be improved by incorporating representation learning techniques that embed biological and chemical knowledge.
蛋白质配体相互作用(PLIs)决定了小分子药物的疗效和安全性。现有方法要么依赖结构信息,要么依赖资源密集型计算来预测PLI,这让人怀疑是否有可能以较低的计算成本进行无结构PLI预测。在这里,我们展示了一种轻量级图神经网络(GNN),它通过对少量蛋白质和配体的定量PLIs进行训练,能够预测未知PLIs的强度。该模型无法直接获取蛋白质配体复合物的结构信息。取而代之的是,通过将整个化学和蛋白质组空间编码成一个单一的异质图,囊括主要蛋白质序列、基因表达、蛋白质-配体相互作用网络以及配体之间的结构相似性,从而提供预测能力。这种新方法的性能可与结构感知模型相媲美,甚至更胜一筹。我们的研究结果表明,通过结合嵌入生物和化学知识的表征学习技术,可以改进现有的 PLI 预测方法。
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引用次数: 0
Elucidating molecular mechanism and chemical space of chalcones through biological networks and machine learning approaches 通过生物网络和机器学习方法阐明查耳酮的分子机制和化学空间
IF 6 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-06 DOI: 10.1016/j.csbj.2024.07.006
Ajay Manaithiya, Ratul Bhowmik, Satarupa Acharjee, Sameer Sharma, Sunil Kumar, Mohd. Imran, Bijo Mathew, Seppo Parkkila, Ashok Aspatwar
We developed a bio-cheminformatics method, exploring disease inhibition mechanisms using machine learning-enhanced quantitative structure-activity relationship (ML-QSAR) models and knowledge-driven neural networks. ML-QSAR models were developed using molecular fingerprint descriptors and the Random Forest algorithm to explore the chemical spaces of Chalcones inhibitors against diverse disease properties, including antifungal, anti-inflammatory, anticancer, antimicrobial, and antiviral effects. We generated and validated robust machine learning-based bioactivity prediction models () for the top genes. These models underwent ROC and applicability domain analysis, followed by molecular docking studies to elucidate the molecular mechanisms of the molecules. Through comprehensive neural network analysis, crucial genes such as and were identified. The PubChem fingerprint-based model revealed key descriptors: PubchemFP521 for , PubchemFP180 for , PubchemFP633 for and PubchemFP145 and PubchemFP338 for , consistently contributing to bioactivity across targets. Notably, chalcone derivatives demonstrated significant bioactivity against target genes, with compound RA1 displaying a predictive pIC value of 5.76 against and strong binding affinities across other targets. Compounds RA5 to RA7 also exhibited high binding affinity scores comparable to or exceeding existing drugs. These findings emphasize the importance of knowledge-based neural network-based research for developing effective drugs against diverse disease properties. These interactions warrant further in vitro and in vivo investigations to elucidate their potential in rational drug design. The presented models provide valuable insights for inhibitor design and hold promise for drug development. Future research will prioritize investigating these molecules for , enhancing the comprehension of effectiveness in addressing infectious diseases.
我们开发了一种生物化学信息学方法,利用机器学习增强型定量结构-活性关系(ML-QSAR)模型和知识驱动神经网络探索疾病抑制机制。我们使用分子指纹描述符和随机森林算法开发了 ML-QSAR 模型,以探索查耳酮抑制剂针对不同疾病特性的化学空间,包括抗真菌、抗炎、抗癌、抗菌和抗病毒作用。我们为顶级基因生成并验证了基于机器学习的稳健生物活性预测模型()。这些模型经过了 ROC 和适用域分析,随后进行了分子对接研究,以阐明分子的分子机制。通过全面的神经网络分析,确定了和等关键基因。基于 PubChem 指纹的模型揭示了关键描述符:PubchemFP521为 ,PubchemFP180为 ,PubchemFP633为 ,PubchemFP145和PubchemFP338为 ,这些描述符一致地对各靶点的生物活性做出了贡献。值得注意的是,查尔酮衍生物对目标基因具有显著的生物活性,化合物 RA1 对目标基因的预测 pIC 值为 5.76,对其他目标基因具有很强的结合亲和力。化合物 RA5 至 RA7 也表现出与现有药物相当或更高的结合亲和力。这些发现强调了以知识为基础的神经网络研究对于开发针对不同疾病特性的有效药物的重要性。这些相互作用需要进一步的体外和体内研究,以阐明它们在合理药物设计中的潜力。所介绍的模型为抑制剂设计提供了宝贵的见解,为药物开发带来了希望。未来的研究将优先研究这些分子,以提高对治疗传染性疾病有效性的理解。
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引用次数: 0
Artificial intelligence in antidiabetic drug discovery: The advances in QSAR and the prediction of α-glucosidase inhibitors 人工智能在抗糖尿病药物研发中的应用:QSAR 和 α-葡萄糖苷酶抑制剂预测的进展
IF 4.4 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-06 DOI: 10.1016/j.csbj.2024.07.003

Artificial Intelligence is transforming drug discovery, particularly in the hit identification phase of therapeutic compounds. One tool that has been instrumental in this transformation is Quantitative Structure-Activity Relationship (QSAR) analysis. This computer-aided drug design tool uses machine learning to predict the biological activity of new compounds based on the numerical representation of chemical structures against various biological targets. With diabetes mellitus becoming a significant health challenge in recent times, there is intense research interest in modulating antidiabetic drug targets. α-Glucosidase is an antidiabetic target that has gained attention due to its ability to suppress postprandial hyperglycaemia, a key contributor to diabetic complications. This review explored a detailed approach to developing QSAR models, focusing on strategies for generating input variables (molecular descriptors) and computational approaches ranging from classical machine learning algorithms to modern deep learning algorithms. We also highlighted studies that have used these approaches to develop predictive models for α-glucosidase inhibitors to modulate this critical antidiabetic drug target.

人工智能正在改变药物发现,尤其是在治疗化合物的命中识别阶段。定量结构-活性关系(QSAR)分析就是在这一变革中发挥重要作用的工具之一。这种计算机辅助药物设计工具利用机器学习,根据针对各种生物靶点的化学结构数字表示来预测新化合物的生物活性。α-葡萄糖苷酶是一个抗糖尿病靶点,因其抑制餐后高血糖的能力而备受关注,而餐后高血糖是糖尿病并发症的主要诱因。本综述探讨了开发 QSAR 模型的详细方法,重点是生成输入变量(分子描述符)的策略以及从经典机器学习算法到现代深度学习算法的计算方法。我们还重点介绍了利用这些方法开发α-葡萄糖苷酶抑制剂预测模型的研究,以调节这一关键的抗糖尿病药物靶点。
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引用次数: 0
Advancing PFAS risk assessment: Integrative approaches using agent-based modelling and physiologically-based kinetic for environmental and health safety 推进全氟辛烷磺酸风险评估:利用基于代理的建模和基于生理动力学的综合方法促进环境和健康安全
IF 6 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 DOI: 10.1016/j.csbj.2024.06.036
Martina Iulini, Giulia Russo, Elena Crispino, Alicia Paini, Styliani Fragki, Emanuela Corsini, Francesco Pappalardo
Per- and polyfluoroalkyl substances (PFAS), ubiquitous in a myriad of consumer and industrial products, and depending on the doses of exposure represent a hazard to both environmental and public health, owing to their persistent, mobile, and bio accumulative properties. These substances exhibit long half-lives in humans and can induce potential immunotoxic effects at low exposure levels, sparking growing concerns. While the European Food Safety Authority (EFSA) has assessed the risk to human health related to the presence of PFAS in food, in which a reduced antibody response to vaccination in infants was considered as the most critical human health effect, a comprehensive grasp of the molecular mechanisms spearheading PFAS-induced immunotoxicity is yet to be attained. Leveraging modern computational tools, including the Agent-Based Model (ABM) Universal Immune System Simulator (UISS) and Physiologically Based Kinetic (PBK) models, a deeper insight into the complex mechanisms of PFAS was sought. The adapted UISS serves as a vital tool in chemical risk assessments, simulating the host immune system's reactions to diverse stimuli and monitoring biological entities within specific adverse health contexts. In tandem, PBK models unravelling PFAS' biokinetics within the body i.e. absorption, distribution, metabolism, and elimination, facilitating the development of time-concentration profiles from birth to 75 years at varied dosage levels, thereby enhancing UISS-TOX's predictive abilities. The integrated use of these computational frameworks shows promises in leveraging new scientific evidence to support risk assessments of PFAS. This innovative approach not only allowed to bridge existing data gaps but also unveiled complex mechanisms and the identification of unanticipated dynamics, potentially guiding more informed risk assessments, regulatory decisions, and associated risk mitigations measures for the future.
全氟烷基和多氟烷基物质(PFAS)在无数消费品和工业产品中无处不在,由于其具有持久性、流动性和生物累积性,根据接触剂量的不同,对环境和公众健康都构成了危害。这些物质在人体内的半衰期较长,在较低的暴露水平下就可能诱发潜在的免疫毒性效应,这引发了越来越多的关注。虽然欧洲食品安全局(EFSA)已经评估了食品中存在的全氟辛烷磺酸对人类健康造成的风险,其中婴儿对疫苗接种的抗体反应降低被认为是对人类健康最关键的影响,但人们尚未全面掌握全氟辛烷磺酸诱导免疫毒性的分子机制。利用现代计算工具,包括基于代理模型(ABM)的通用免疫系统模拟器(UISS)和基于生理动力学(PBK)的模型,我们试图更深入地了解 PFAS 的复杂机制。经过调整的通用免疫系统模拟器是化学品风险评估的重要工具,它可以模拟宿主免疫系统对各种刺激的反应,并监测特定不利健康环境下的生物实体。与此同时,PBK 模型揭示了 PFAS 在人体内的生物动力学,即吸收、分布、代谢和消除,促进了在不同剂量水平下从出生到 75 岁的时间浓度曲线的发展,从而增强了 UISS-TOX 的预测能力。这些计算框架的综合使用表明,利用新的科学证据支持全氟辛烷磺酸风险评估大有可为。这种创新方法不仅弥补了现有的数据缺口,还揭示了复杂的机制,并确定了意料之外的动态变化,有可能为未来更明智的风险评估、监管决策和相关风险缓解措施提供指导。
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引用次数: 0
Developing the PIP-eco: An integrated genomic pipeline for identification and characterization of Escherichia coli pathotypes encompassing hybrid forms 开发 PIP-eco:用于鉴定和描述包括杂交型大肠埃希菌病型的综合基因组管道
IF 4.4 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 DOI: 10.1016/j.csbj.2024.07.017
Seyoung Ko, Huynh Minh Triet Nguyen, Woojung Lee, Donghyuk Kim
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引用次数: 0
Enhancing prediction of short linear protein motifs with Wregex 3.0 利用 Wregex 3.0 加强对短线性蛋白质主题的预测
IF 4.4 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 DOI: 10.1016/j.csbj.2024.07.013
Gorka Prieto, Jose A. Rodríguez, A. Fullaondo
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引用次数: 0
Usability of the BigO system in pediatric obesity treatment: A mixed-methods evaluation of clinical end-users BigO 系统在儿科肥胖症治疗中的可用性:对临床最终用户的混合方法评估
IF 4.4 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-07-01 DOI: 10.1016/j.csbj.2024.06.034

Objective

To assess technical usability of the BigO app and clinical portal among diverse participants and explore the overall user experiences of both.

Methods

Methods included technical usability testing by measuring the relative user efficiency score (RUS) for the app and measuring Relative User Efficiency (RUE) using the ‘think aloud’ method with the clinical portal. Qualitative approaches involved focus groups with adolescent app users and semi-structured one-to-one interviews with clinician participants. Thematic analysis was applied to analyze qualitative data.

Participants

Clinical participants consisted of adolescents seeking treatment for severe obesity and were invited via telephone/face to face to attend technical usability testing and a focus group. Healthcare professionals (HCPs) and researchers using the BigO clinical portal interface were invited to participate in usability testing and semi-structured interviews.

Results

From 14 families invited to attend, seven consented to join the study and four adolescents (mean age=13.8 (SD 0.8) years) participated. Additionally, six HCPs and one pediatric obesity researcher took part. RUS for adolescents indicated that the tasks required of them via myBigO app were feasible, and technically efficient. No user-related errors were observed during tasks. Technical barriers reported by adolescents included notifications of battery optimization, misunderstanding image annotation language, and compatibility challenges with certain phone models. RUS for the HCPs and researcher indicated that basic technical skills are a potential barrier for clinical portal use and qualitative findings revealed that clinical users wanted a logging option for monitoring goals and providing feedback on the portal.

Conclusion

Our study provided valuable formative findings from clinical end-users in Ireland indicating that adolescents being treated for obesity rated myBigO app as usable, acceptable and that it may assist other key stakeholders to understand food marketing and to monitor dietary and physical activity behaviors. Several key suggestions for future iterations of the clinical portal were provided to enhance its value in pediatric obesity treatment.

方法包括通过测量应用程序的相对用户效率得分(RUS)进行技术可用性测试,以及使用 "大声思考 "法测量临床门户网站的相对用户效率(RUE)。定性方法包括与青少年应用程序用户进行焦点小组讨论,以及与临床医生参与者进行半结构化一对一访谈。临床参与者包括因严重肥胖而寻求治疗的青少年,他们通过电话/面对面的方式被邀请参加技术可用性测试和焦点小组。结果14个受邀家庭中,7个同意参加研究,4名青少年(平均年龄=13.8(SD 0.8)岁)参加了研究。此外,六名保健医生和一名儿科肥胖症研究人员也参与了研究。针对青少年的 RUS 表明,通过 myBigO 应用程序要求他们完成的任务是可行的,而且在技术上是有效的。在任务执行过程中未发现与用户相关的错误。青少年报告的技术障碍包括电池优化通知、对图像注释语言的误解以及与某些手机型号的兼容性问题。针对保健医生和研究人员的 RUS 表明,基本的技术技能是临床门户网站使用的潜在障碍,定性研究结果表明,临床用户希望有一个日志选项来监控目标并提供门户网站上的反馈。为临床门户网站的未来迭代提出了一些重要建议,以提高其在儿科肥胖症治疗中的价值。
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引用次数: 0
Mime: A flexible machine-learning framework to construct and visualize models for clinical characteristics prediction and feature selection Mime:灵活的机器学习框架,用于构建和可视化临床特征预测和特征选择模型
IF 6 2区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-06-29 DOI: 10.1016/j.csbj.2024.06.035
Hongwei Liu, Wei Zhang, Yihao Zhang, Abraham Ayodeji Adegboro, Deborah Oluwatosin Fasoranti, Luohuan Dai, Zhouyang Pan, Hongyi Liu, Yi Xiong, Wang Li, Kang Peng, Siyi Wanggou, Xuejun Li
The widespread use of high-throughput sequencing technologies has revolutionized the understanding of biology and cancer heterogeneity. Recently, several machine-learning models based on transcriptional data have been developed to accurately predict patients’ outcome and clinical response. However, an open-source R package covering state-of-the-art machine-learning algorithms for user-friendly access has yet to be developed. Thus, we proposed a flexible computational framework to construct a machine learning-based integration model with elegant performance (Mime). Mime streamlines the process of developing predictive models with high accuracy, leveraging complex datasets to identify critical genes associated with prognosis. An in silico combined model based on de novo PIEZO1-associated signatures constructed by Mime demonstrated high accuracy in predicting the outcomes of patients compared with other published models. Furthermore, the PIEZO1-associated signatures could also precisely infer immunotherapy response by applying different algorithms in Mime. Finally, SDC1 selected from the PIEZO1-associated signatures demonstrated high potential as a glioma target. Taken together, our package provides a user-friendly solution for constructing machine learning-based integration models and will be greatly expanded to provide valuable insights into current fields. The Mime package is available on GitHub ().
高通量测序技术的广泛应用彻底改变了人们对生物学和癌症异质性的认识。最近,一些基于转录数据的机器学习模型被开发出来,用于准确预测患者的预后和临床反应。然而,目前尚未开发出一个开源的 R 软件包,它涵盖了最先进的机器学习算法,方便用户使用。因此,我们提出了一个灵活的计算框架,以构建一个基于机器学习、性能优雅的整合模型(Mime)。Mime 简化了开发高精度预测模型的过程,利用复杂的数据集来识别与预后相关的关键基因。与其他已发表的模型相比,Mime 构建的基于全新 PIEZO1 相关特征的硅学组合模型在预测患者预后方面表现出极高的准确性。此外,PIEZO1相关特征还能通过Mime中的不同算法精确推断免疫治疗反应。最后,从 PIEZO1 相关特征中筛选出的 SDC1 显示出作为胶质瘤靶点的巨大潜力。总之,我们的软件包为构建基于机器学习的整合模型提供了用户友好型解决方案,并将得到极大扩展,为当前领域提供有价值的见解。Mime 软件包可在 GitHub 上下载()。
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引用次数: 0
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